package org.cbioportal.legacy.web;

import io.swagger.v3.oas.annotations.Operation;
import io.swagger.v3.oas.annotations.Parameter;
import io.swagger.v3.oas.annotations.media.ArraySchema;
import io.swagger.v3.oas.annotations.media.Content;
import io.swagger.v3.oas.annotations.media.Schema;
import io.swagger.v3.oas.annotations.responses.ApiResponse;
import io.swagger.v3.oas.annotations.tags.Tag;
import java.util.List;
import org.cbioportal.legacy.model.GenesetMolecularData;
import org.cbioportal.legacy.service.GenesetDataService;
import org.cbioportal.legacy.service.exception.MolecularProfileNotFoundException;
import org.cbioportal.legacy.service.exception.SampleListNotFoundException;
import org.cbioportal.legacy.web.config.annotation.InternalApi;
import org.cbioportal.legacy.web.parameter.GenesetDataFilterCriteria;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.security.access.prepost.PreAuthorize;
import org.springframework.validation.annotation.Validated;
import org.springframework.web.bind.annotation.PathVariable;
import org.springframework.web.bind.annotation.RequestBody;
import org.springframework.web.bind.annotation.RequestMapping;
import org.springframework.web.bind.annotation.RequestMethod;
import org.springframework.web.bind.annotation.RestController;

@InternalApi
@RestController()
@RequestMapping("/api")
@Validated
@Tag(name = "Gene Set Scores", description = " ")
public class GenesetDataController {

  @Autowired private GenesetDataService genesetDataService;

  @PreAuthorize(
      "hasPermission(#geneticProfileId, 'GeneticProfileId', T(org.cbioportal.legacy.utils.security.AccessLevel).READ)")
  @RequestMapping(
      value = "/genetic-profiles/{geneticProfileId}/geneset-genetic-data/fetch",
      method = RequestMethod.POST,
      consumes = MediaType.APPLICATION_JSON_VALUE,
      produces = MediaType.APPLICATION_JSON_VALUE)
  @Operation(
      description =
          "Fetch gene set \"genetic data\" items (gene set scores) by profile Id, gene set ids and sample ids")
  @ApiResponse(
      responseCode = "200",
      description = "OK",
      content =
          @Content(
              array = @ArraySchema(schema = @Schema(implementation = GenesetMolecularData.class))))
  public ResponseEntity<List<GenesetMolecularData>> fetchGeneticDataItems(
      @Parameter(required = true, description = "Genetic profile ID, e.g. gbm_tcga_gsva_scores")
          @PathVariable
          String geneticProfileId,
      @Parameter(
              required = true,
              description =
                  "Search criteria to return the values for a given set of samples and gene set items. "
                      + "genesetIds: The list of identifiers for the gene sets of interest, e.g. HINATA_NFKB_MATRIX. "
                      + "Use one of these if you want to specify a subset of samples:"
                      + "(1) sampleListId: Identifier of pre-defined sample list with samples to query, e.g. brca_tcga_all "
                      + "or (2) sampleIds: custom list of samples or patients to query, e.g. TCGA-BH-A1EO-01, TCGA-AR-A1AR-01")
          @RequestBody
          GenesetDataFilterCriteria genesetDataFilterCriteria)
      throws MolecularProfileNotFoundException, SampleListNotFoundException {

    if (genesetDataFilterCriteria.getSampleListId() != null
        && genesetDataFilterCriteria.getSampleListId().trim().length() > 0) {
      return new ResponseEntity<>(
          genesetDataService.fetchGenesetData(
              geneticProfileId,
              genesetDataFilterCriteria.getSampleListId(),
              genesetDataFilterCriteria.getGenesetIds()),
          HttpStatus.OK);
    } else {
      return new ResponseEntity<>(
          genesetDataService.fetchGenesetData(
              geneticProfileId,
              genesetDataFilterCriteria.getSampleIds(),
              genesetDataFilterCriteria.getGenesetIds()),
          HttpStatus.OK);
    }
  }
}
